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Condensed Consolidated Statements of Cash Flows (USD $)
In Thousands, unless otherwise specified
 3 Months Ended 277 Months Ended
Mar. 31, 2014
Mar. 31, 2013
Mar. 31, 2014
CASH FLOWS FROM OPERATING ACTIVITIES:      
Net loss $ (52,056) $ (40,965) $ (2,348,458)
Adjustments to reconcile net loss to net cash used in operating activities:      
Depreciation and accretion 9,394 3,348 150,228
Stock-based compensation expense 10,937 5,189 194,042
Stock expense for shares issued pursuant to research agreement     3,018
(Gain) loss on sale, abandonment/disposal or impairment of property and equipment     25,070
Accrued interest on investments, net of amortization of discounts     (191)
In-process research and development     19,726
Goodwill impairment     151,428
Loss on available-for-sale securities     990
Litigation settlement in stock     6,494
Fair value of forward purchase contract     1,237
Other, net   (2) 1,101
Changes in assets and liabilities:      
State research and development credit exchange receivable (82) (78) (379)
Prepaid expenses and other current assets 1,845 690 (1,690)
Other assets     (230)
Accounts payable (1,038) (924) 2,309
Accrued expenses and other current liabilities (6,704) 715 32,019
Other liabilities 714   1,303
Net cash used in operating activities (36,990) (32,027) (1,761,983)
CASH FLOWS FROM INVESTING ACTIVITIES:      
Purchase of marketable securities     (796,779)
Sales and maturities of marketable securities     796,393
Purchase of property and equipment (1,409) (1,459) (337,142)
Proceeds from sale of property and equipment     454
Net cash used in investing activities (1,409) (1,459) (337,074)
CASH FLOWS FROM FINANCING ACTIVITIES:      
Issuance of common stock and warrants, net of issuance costs 1,463 78 1,451,640
Collection of Series C convertible preferred stock subscriptions receivable     50,000
Issuance of Series B convertible preferred stock for cash     15,000
Cash received for common stock to be issued     3,900
Repurchase of common stock     (1,028)
Put shares sold to majority stockholder     623
Exercise of warrants for common stock 1,938   96,085
Borrowings under lines of credit     4,220
Payment of 2013 notes     (115,000)
Proceeds from notes receivables     1,742
Proceeds from issuance of facility financing obligation & milestone rights     119,500
Facility financing obligation & milestone rights issuance costs     (598)
Borrowings on notes payable to principal stockholder     387,750
Principal payments on notes payable to principal stockholder     (70,000)
Borrowings on notes payable     3,460
Principal payments on notes payable     (1,667)
Proceeds from senior convertible notes     207,050
Payment of employment taxes related to vested restricted stock units (33) (427) (17,861)
Net cash provided by (used in) financing activities 3,368 (349) 2,134,816
NET INCREASE (DECREASE) IN CASH AND CASH EQUIVALENTS (35,031) (33,835) 35,759
CASH AND CASH EQUIVALENTS, BEGINNING OF PERIOD 70,790 61,840  
CASH AND CASH EQUIVALENTS, END OF PERIOD 35,759 28,005 35,759
SUPPLEMENTAL CASH FLOWS DISCLOSURES:      
Cash paid for income taxes     26
Interest paid in cash, net of amounts capitalized 4,678 2,863 77,282
Accretion on redeemable convertible preferred stock     (952)
Issuance of common stock upon conversion of notes payable     3,331
Increase in additional paid-in capital resulting from merger     171,154
Issuance of common stock for notes receivable     2,758
Issuance of common stock pursuant to conversion of facility financing obligation 86,000   92,500
Issuance of put option by stockholder     (2,949)
Put option redemption by stockholder     1,921
Issuance of Series C convertible preferred stock subscriptions     50,000
Issuance of Series A redeemable convertible preferred stock     4,296
Conversion of Series A redeemable convertible preferred stock     (5,248)
Non-cash construction in progress and property and equipment 1,700 3,863 1,700
Capitalization of interest on note payable to principal stockholder     22,105
Reduction of principal on note payable to principal stockholder upon issuance of common stock and exercise of warrants     290,334
Forward purchase contract contribution to APIC     29,317
Reclassification of forward purchase contract to APIC     28,080
Tranche B Commitment Asset $ 2,921   $ 2,921